Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session A29: Experimental Techniques in Biophysics |
Hide Abstracts |
Sponsoring Units: DBP Chair: J. P. Landry, University of California, Davis Room: Baltimore Convention Center 326 |
Monday, March 13, 2006 8:00AM - 8:12AM |
A29.00001: The healing mechanism for excited molecules near metallic surfaces B. Barbiellini, P.M. Platzman Radiation damage prevents the ability to obtain images from individual molecules. We suggest that this problem can be avoided for organic molecules by placing them in close proximity with a metallic surface. The molecules will then quickly dissipate any electronic excitation via their coupling to the metal surface. They may therefore be observed for a number of elastic scattering events that is sufficient to determine their structure.\\ \mbox{[1] B. Barbiellni and P. M. Platzman, cond-mat/0506403} [Preview Abstract] |
Monday, March 13, 2006 8:12AM - 8:24AM |
A29.00002: Pulse-shaping and Fourier Transform Techniques in Multiphoton Microscopy Jennifer Ogilvie, Delphine D\'{e}barre, Emmanuel Beaurepaire, Antigoni Alexandrou, Manuel Joffre Multiphoton microscopy is an important tool that is increasingly used in biological research. The ease with which broadband femtosecond pulses can be created and manipulated has opened up new directions for enhancing multiphoton microscopy. In particular, pulse-shaping techniques can tailor broadband light to selectively excite fluorescent species.[1] Here we demonstrate the use of pulse-shaped excitation to enhance multiphoton fluorescence imaging of live drosophila embryos. Other promising multiphoton techniques include coherent anti-Stokes Raman scattering (CARS) microscopy, which offers endogenous contrast based on the inherent vibrations of different chemical species.[2]~Most implementations of CARS microscopy image single vibrational modes, providing limited ability to simultaneously follow multiple chemical species. An alternate time-domain Fourier transform-based method can produce spectrally resolved CARS images over the considerable bandwidth of a broadband laser source, This approach provides straightforward removal of the nonresonant background from CARS images while offering a compact, single-laser approach. [1] V. V. Lozovoy et al. J. Chem. Phys, (2003) 118, 3187. [2] A. Zumbusch et al. Phys. Rev. Lett. (1999) 82 4142. [Preview Abstract] |
Monday, March 13, 2006 8:24AM - 8:36AM |
A29.00003: Templated biomineralization on self assembled protein fibers S. Palmaccio, K. Subburaman, N. Pernodet, S.-Y. Kwak, E. DiMasi, S. Ge, N.L. Yang, M. Rafailovich We have previously shown that fibrillogenesis of extracellular matrix (ECM) proteins like Fibronectin and Elastin can be induced when adsorbed on charged polymer surfaces. These self assembled fiber networks reach sizes of dimensions similar to natural ECM. Here we present a study of biomineralization on these protein fibers, achieved using CaCO$_{3}$ through Kitano {\&} Flow cell methods. The mechanical properties were measured using$_{ }$Shear Modulation Force Microscopy (SMFM) as part of early stage mineralization studies. Results indicated increase in modulus with exposure time on fibers, with no increase off the fibers. Control studies with other Ca salts showed no change in fiber modulus, differentiating mineralization from salt adsorption. Late Stage Mineralization studied using ToF SIMS showed preferential Ca adsorption on the fibers. Optical Microscopy also showed preferential crystal formation on fibers. TEM was used to identity the crystal structure and orientation. Effect of proteins on crystal orientation and mineralization of natural ECM from osteoblasts are under study. Supported by USDOE Contract No DE-AC02-98CH10886, NSF-MRSEC {\&} BNL-SBU Seed Grant. [Preview Abstract] |
Monday, March 13, 2006 8:36AM - 8:48AM |
A29.00004: Advances in energy filtered electron tomography for quantitative 3-D phosphorus imaging of cell nuclei Maria A. Aronova, Guofeng Zhang, Richard D. Leapman Electron tomography (ET) is an established and valuable tool for determining three-dimensional subcellular structure at a macromolecular scale. Contrast in conventional tomograms is generated through high-angle elastic scattering of the incident electrons by heavy atoms in stained plastic sections or through phase differences of elastic scattering in frozen hydrated specimens. Energy filtered transmission electron microscopy (EFTEM) has undergone recent developments to provide an improved capability for quantitative mapping of elemental distributions. We have developed a new approach where specific chemical elements in biological systems can be imaged in three dimensions. This method of collecting electron tomograms with inelastically scattered electrons combines ET and EFTEM. We have applied this technique to analyze unstained sections of rapidly frozen, freeze-substituted and embedded cells. Using intrinsic phosphorus as a label for nucleic acid, we have investigated the distribution of DNA in nuclei of \textit{Drosophila} larvae. We show that quantitative analysis of the three-dimensional phosphorus distribution has the potential to provide new information about the DNA packing density of chromatin. [Preview Abstract] |
Monday, March 13, 2006 8:48AM - 9:00AM |
A29.00005: Adaptive wave-front correction for multi-photon microscopy using coherence-gated wave-front sensing Markus Rueckel, Winfried Denk The contrast and the resolution of a multi-photon microscope highly depend on the shape of the focus which can be distorted by refractive index inhomogeneities within the specimen. Coherence-gated wave-front sensing (CGWS) allows reliable adaptive wave-front correction of these distortions (M. Feierabend, M. Ruckel, and W. Denk, Optics Letters, 2004, 29(19)). We developed a model for CGWS for which we evaluated in detail, using Monte-Carlo simulations, how the measured wave-fronts depend on the density of scatterers, the position and length of the coherence gate, and on the polarization of the light used. Predictions from this model were confirmed experimentally. Further we report on early results from an exploration of how much the two-photon excitation efficiency improves when applying corrections as predicted by CGWS. Experiments and numerical simulations show for a wave-front with a RMS distortion of $\lambda $/5 that the excitation efficiency was about 60{\%} of that for a diffraction-limited focus. This was done for both astigmatism and coma. [Preview Abstract] |
Monday, March 13, 2006 9:00AM - 9:12AM |
A29.00006: Label-free optical detection of protein binding on small-molecule ligand microarrays Y. S. Sun, J. P. Landry, X. D. Zhu, T. Bao, K. S. Lam Biomolecular microarrays are becoming indispensable tools in proteomic research and biomarker discovery processes. The need for label-free microarray detection methods that are complementary to fluorescence-based methods is also increasing. We have developed oblique-incidence reflectivity difference (OI-RD) microscopes for detecting protein-protein and protein-small molecule reactions in microarray format through changes in density, thickness, and conformation of surface-bound proteins on solid supports. This can be done without extrinsic labeling molecules (e.g. organic fluorophores or quantum dots), which are costly and potentially intrusive. Of particular interest to one of our current investigations are microarrays of small molecules that may be used for high-throughput screening for protein ligands. With OI-RD microscopes, we have detected antibody-antigen capture and streptavidin-biotin binding reactions in microarray format using mixtures of proteins as well as pure proteins in prescribed sequences. In the streptavidin-biotin binding reaction, we used BSA molecules as the scaffold to anchor biotin molecules on the solid support. We will report these recent experimental results and the analysis. [Preview Abstract] |
Monday, March 13, 2006 9:12AM - 9:24AM |
A29.00007: Dynamic Dimensional Analysis of \textit{In-Vivo} Microorganisms Using Polarized Light Scattering Willem Van De Merwe, Jozsef Czege We have successfully determined average lengths and diameters of randomly-oriented rod-shaped bacteria in-vivo by evaluating the Mueller matrix ratio $<$S$_{34}>$/$<$S$_{11}>$ together with Coulter counter measurements of cell volumes (references 1 and 2.) We showed that our technique allows one to follow real-time dimensional changes taking place at a rate of about 14 nm/min. We expect to extend this method to synchronized cultures and will attempt to measure changes in the ratio for partially aligned bacterial cells. We will give a rationale for our expectation that this will provide additional information for example about growth characteristics of the bacteria. We used the coupled dipole model to compare theoretical predictions and experimental observations. Specifically, by refining our dimensional analysis we expect soon to be able to study the dynamic of bacterial cell division real-time as well as obtain additional identifying signatures of importance to medicine, biotechnology and detection. \underline {1) }Applied Optics \underline {43} (2004) 5295-5302 \underline {2) }Biophysical J. \underline {69} (1995) 1170-1177 [Preview Abstract] |
Monday, March 13, 2006 9:24AM - 9:36AM |
A29.00008: Fast Cooling and Vitrification of Aqueous Solutions for Cryopreservation Matt Warkentin, Naji Husseini, Viatcheslav Berejnov, Robert Thorne In many applications, a small volume of aqueous solution must be cooled at a rate sufficient to produce amorphous solid water.~ Two prominent examples include flash-freezing of protein crystals for X-ray data collection and freezing of cells (i.e. spermatozoa) for cryopreservation.~ The cooling rate required to vitrify pure water ($\sim $10$^{6}$ K/s) is unattainable for volumes that might contain cells or protein crystals, but the required rate can be reduced by adding cryoprotectants. We report the first measurements of the critical concentration required to produce a vitrified sample as a function of the sample's volume, the cryogen into which the sample is plunged, and the temperature of the cryogen, for a wide range of cryoprotectants.~ These experiments have broad practical consequences for cryopreservation, and provide insight into the physics of glass formation in aqueous systems. [Preview Abstract] |
Monday, March 13, 2006 9:36AM - 9:48AM |
A29.00009: Active and Passive Microscopic Viscoelastic Response in Poly(Ethylene) Oxide Solutions Olga Latinovic, H. Daniel Ou-Yang It has been proposed that one can determine the viscoelastic response function from the thermal fluctuations of colloidal tracer particles. Despite attempts to validate the approach, there has not been a direct comparison between the viscoelastic response obtained by thermally driven particles, and independent microscopic measurements which do not depend on thermal fluctuations. This paper reports a study that compares the two approaches. In the passive measurements, the Brownian motion of a probe particle was used to obtain the viscoelastic modulus of poly (ethylene) oxide solutions using the fluctuation-dissipation theorem and the generalized Stokes-Einstein relation. In the active measurements, the same probe particle is set into forced oscillations by oscillating optical tweezers and the viscoelastic moduli of the solution are obtained from the in-phase and out-of-phase components of the particle's motion. [Preview Abstract] |
Monday, March 13, 2006 9:48AM - 10:00AM |
A29.00010: Specifically Detect Vascular Endothelia Growth Factor (VEGF) with Micro Cantilever Resonator Jianhua Gu, Debin Li, David Lederman, Jarod Kabulski, Peter Gannett, Daniel Flynn VEGF is an important protein marker for lung cancer. Current state of the art detection strategies use enzyme linked immunosorbent assays (ELISA), where only nanogram levels can be detected in serum. We have developed a sensing method to rapidly detect VEGF based on the micro cantilever resonator technique, which has advantages over the standard ELISA method. We have covalently linked a polyclonal anti-VEGF antibody to a silicon cantilever surface. The shift of cantilever resonant frequency due to specific VEGF binding with this antibody allows us to detect the presence of VEGF in solution at detection levels of approximately one picogram or even smaller. Efforts were made to reduce nonspecific adsorption on cantilever either by covering non-specific sites on the cantilever with proteins (such as bovine serum albumin (BSA)), or by self-assembly of a protein resistant monolayer on the cantilever surface. We also used different protein samples (like VEGF-C or MMP-9) to confirm the specific detection of VEGF. [Preview Abstract] |
Monday, March 13, 2006 10:00AM - 10:12AM |
A29.00011: Serial Crystallography: imaging single proteins at a synchrotron David Shapiro, John Spence, R. Bruce Doak, Dmitri Starodub, Uwe Weierstal, Henry Chapman, Stefano Marchesini, Malcolm Howells A new method is proposed for the imaging of uncrystallized proteins at third generation x-ray sources. The method, serial crystallography, uses the diffraction pattern produced by a beam of hydrated proteins as they sequentially traverse a continuous x-ray beam after having been aligned by an intense laser field. Each particle is exposed to the x-ray beam so briefly that radiation damage is not a concern. The diffraction pattern is integrated as many identically aligned particles cross the beam and then the laser polarization is rotated to allow collection of other particle orientations. The diffraction pattern can then be phased by an iterative algorithm and the protein structure recovered with a Fourier transform. We are currently constructing a serial crystallography apparatus to be installed on beamline 9.0.1 of the Advanced Light Source at Lawrence Berkeley National Lab that will be operational by May, 2006. Preliminary experiments will use a 5 Watt CW IR laser to align particles of Tobacco Mosaic Virus and their soft x-ray diffraction patterns will be collected. We present the design of the serial crystallography apparatus and the current status of this project. [Preview Abstract] |
Monday, March 13, 2006 10:12AM - 10:24AM |
A29.00012: Structural investigations of human hairs by spectrally resolved ellipsometry Benjamin Schulz, D. Chan, M. Ruebhausen, S. Wessel, R. Wepf Human hair is a biological layered system composed of two major layers, the cortex and the cuticle. We show spectrally resolved ellipsometry measurements of the ellipsometric parameters $\Psi$ and $\Delta$ of single human hairs. The spectra reflect the layered nature of hair and the optical anisotropy of the hair’s structure. In addition, measurements on strands of human hair show a high reproducibility of the ellipsometric parameters for different hair fiber bundles from the same person. Based on the measurements, we develop a model of the dielectric function of hair that explains the spectra. This model includes the dielectric properties of the cuticle and cortex as well as their associated layer thicknesses. In addition, surface roughness effects modelled by a roughness layer with an complex refractive index given by an effective medium approach can have a significant effect on the measurements. We derive values for the parameters of the cuticle surface roughness layer of the thickness $d_{ACu} = 273-360\quad\text{nm}$ and the air inclusion $f_{A} = 0.6 -5.7\%$. [1] accepted for publication in J. Biomed Opt., 2005 [Preview Abstract] |
Monday, March 13, 2006 10:24AM - 10:36AM |
A29.00013: Evanescent Wave Excitation and Raman Spectroscopy of Bacteriorhodopsin on Gallium Nitride Waveguide Structures Alfons Schulte, Sonya Ortiz, Alfred Keller, April Pope, Yu Guo, Heidi Hockel, Eric Johnson Composite structures of protein-semiconductor layers have potential for molecular electronics and sensor applications. We investigate gallium nitride waveguide structures created by UV lithographic techniques as substrates for photoactive bacteriorhodopsin films. The waveguides were characterized through electron and optical interference microscopy. The top biomolecular layer is optically accessible through the evanescent field of a mode propagating in the gallium nitride waveguide. A 488 nm or 514 nm beam from an Argon ion laser was coupled into the waveguide and the evanescent field was employed to initiate the photocycle and excite Raman scattering in the bacteriorhodopsin film. Under stationary conditions the Raman spectrum in the fingerprint region shows the presence of the light-adapted state and the M intermediate. This suggests that the protein is in its native state and that optical switching of bacteriorhodopsin can be achieved and probed by evanescent wave excitation. [Preview Abstract] |
Monday, March 13, 2006 10:36AM - 10:48AM |
A29.00014: Probing Protein Structural Dynamics Using Microfluidic Diffusional Mixer Based FT-MIR Micro-Spectroscopy Peter Galajda, Robert Austin, Jarmila Gurjarro, Jesus Vega, Cyrus Arian, Aihua Xie Time-resolved Fourier transform Infrared (FTIR) spectroscopy is a powerful technique to ``see'' proteins in action. Such a technique has been mostly applied to study photoreceptor proteins since their biological functions can be conveniently triggered in synchronization using short laser pulses. However, only a few proteins in nature are photo-active. In order to study a broad range of chemically activated proteins, we have developed a microfluidic diffusional mixing device, based on computational modeling of microfluidic flow and advection diffusion, microlithographic fabrication, and time-resolved FTIR micro-spectroscopy. This technique can be applied to probe functionally important structural dynamics of proteins that are chemically activated, thus opening up a broader application of time-resolved FTIR spectroscopic techniques. We will report such applications including experimental studies on GTPase system in biological signal transduction. [Preview Abstract] |
Monday, March 13, 2006 10:48AM - 11:00AM |
A29.00015: Modeling Electric Fields of Peripheral Nerve Block Needles. James Ch. Davis, Norman E. Anderson, Mark W. Meisel, Jason G. Ramirez, F. Kayser Enneking Peripheral nerve blocks present an alternative to general anesthesia in certain surgical procedures and a means of acute pain relief through continuous blockades. They have been shown to decrease the incidence of postoperative nausea and vomiting, reduce oral narcotic side effects, and improve sleep quality. Injecting needles, which carry small stimulating currents, are often used to aid in locating the target nerve bundle. With this technique, muscle responses indicate needle proximity to the corresponding nerve bundle. Failure rates in first injection attempts prompted our study of electric field distributions. Finite difference methods were used to solve for the electric fields generated by two widely used needles. Geometric differences in the needles effect variations in their electric field and current distributions. Further investigations may suggest needle modifications that result in a reduction of initial probing failures. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700